Quick Overview

A Quick Overview of our ATOL Project

Goal: To develop a demonstration prototype of a service-oriented architecture enabling and supporting morphologically based phylogenetic studies.

Key components include:

  1. Define the structure of and develop software for the management of morphological ontologies, including image-based documentation of scientific concepts for morphological elements (parts) and individual characters and character states.
  2. Testing and deployment of the system in item 1 populated with morphology and character states derived from ongoing ATOL and phylogeny projects in fishes.  Additionally a Post-Doctoral Fellow hired with funds created by the overhead reduction provided by UT will be hired to complete a fully populated ontology with characters and character states for ….
  3. Development and/or integration (from Morphbank) of a system for controlled, (ontology-based) image labeling and annotation of morphological features and character states.
  4. A character management system (e.g. an electronic notebook) for incorporating annotated images and character state documentation into phylogenetic studies (ie. a matrix manager).

The system will be distributed and collaborative.  For the service-oriented architecture a SOAP infrastructure will be explored.  A primary scientific issue is the complete and consistent distributed representation of ontologies (both taxonomic and morphological).  The use of the LSID global identifier system will be explored as the implementation mechanism.

The system will target integration with, or seek to be consistent with the following external interfaces and source of data:

  1.  Taxonomic Name Services
    • NCBI Taxonomy
    • Rod Pages Taxonomic Search Engine
    • SEEK Taxonomic Object Service
  2. TDWG and GBIF efforts concerning biodiversity data (ABCD/Darwin core) and descriptive specimen data (SDD).
  3. CIPRes and Treebase repositories for data matrices (XML version of Nexus files).